The effect of LC-MS data preprocessing methods on the selection of plasma biomarkers in fed vs. fasted rats
Open accessAbstract
The metabolic composition of plasma is affected by time passed since the last meal and by individual variation in metabolite clearance rates. Rat plasma in fed and fasted states was analyzed with liquid chromatography quadrupole-time-of-flight mass spectrometry (LC-QTOF) for an untargeted investigation of these metabolite patterns. The dataset was used to investigate the effect of data preprocessing on biomarker selection using three different softwares, MarkerLynxTM, MZmine, XCMS along with a customized preprocessing method that performs binning of m/z channels followed by summation through retention time. Direct comparison of selected features representing the fed or fasted state showed large differences between the softwares. Many false positive markers were obtained from custom data preprocessing compared with dedicated softwares while MarkerLynxTM provided better coverage of markers. However, marker selection was more reliable with the gap filling (or peak finding) algorithms present in MZmine and XCMS. Further identification of the putative markers revealed that many of the differences between the markers selected were due to variations in features representing adducts or daughter ions of the same metabolites or of compounds from the same chemical subclasses, e.g., lyso-phosphatidylcholines (LPCs) and lyso-phosphatidylethanolamines (LPEs). We conclude that despite considerable differences in the performance of the preprocessing tools we could extract the same biological information by any of them. Carnitine, branched-chain amino acids, LPCs and LPEs were identified by all methods as markers of the fed state whereas acetylcarnitine was abundant during fasting in rats.
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There is only a 50-70% overlap between peaks detected by different software packages from the same raw data set, even with similar settings.
“There is only a 50-70% overlap between the peaks detected by different packages from the same raw data set, even with similar settings (125).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [125]
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The food metabolome: a window over dietary exposure
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- Authors
- Gürdeniz, G., Kristensen, M., Skov, T., & Dragsted, L. O.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Gürdeniz, Gözde
- Venue
- Metabolites
- Publisher
- MDPI AG
- Published
- 2012-01-18
- Volume
- 2
- Issue
- 1
- Pages
- 77-99
- ISSN
- 2218-1989 (ISSN-L)
- PMC
- PMC3901197
- OpenAlex
- W2142931933
- Cited by
- 61
- References
- 40
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 4 · 2022: 2 · 2021: 8 · 2020: 3 · 2019: 5 · 2018: 8 · 2017: 4 · 2016: 4 · 2015: 2 · 2014: 6 · 2013: 10 · 2012: 3
- FWCI
- 2.70
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Metabolites (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- plasma biomarkers, data preprocessing, MZmine, XCMS, untargeted metabolomics, lysophosphatidylcholine, lysophosphatidylethanolamine, L-carnitine, acetyl-L-carnitine, branched-chain amino acids, rats
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